This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Core 2 seeks to improve proteome analyses through a multitude of technological advancements. These advancements have been achieved by extending the capabilities to include non-conventional nanogram-sized and smaller samples, by enhancing the dynamic range of the MS measurements, by applying new methods of analyzing intact proteins, by developing an artificial neural network to predict peptide retention times during strong cation exchange chromatography, by improving stable isotope labeling with oxygen-18, by implementing a universal reference standard for quantification, by increasing the sensitivity of targeted quantitative proteomics when applying MRM measurements, by developing a multiplexed quantification strategy for phosphopeptides, by applying a "next generation" proteomics LC-IMS-MS instrument platform developed with the help of the Center for increasing the overall peak capacity of a proteomics system, by improving biofluid proteome coverage, and by making additional advances in MS sensitivity.